Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy

Trends in synonymous codon usage in adenoviruses have been examined through the multivariate statistical analysis on the annotated protein-coding regions of 22 adenoviral species, for which complete genome sequences are available. One of the major determinants of such trends is the G+C content at third codon positions of the genes, the average value of which varied from one viral genome to other depending on the overall mutational bias of the species. G3S and C3S interacted synergistically along the first principal axis of correspondence analysis on the Relative Synonymous Codon Usage of adenoviral genes, but antagonistically along the second principal axis. The intra-genomic variation in codon usage pattern in adenoviruses is generally influenced by asymmetrical mutational bias in two DNA strands. Other major determinants of the trends are the natural selection, putatively operative at the level of translation and quite interestingly, hydropathy of the encoded proteins. The trends in codon usage, though characterized by distinct virus-specific mutational bias, do not exhibit any sign of host-specificity. Significant variations are observed in synonymous codon choice in structural and nonstructural genes of adenoviruses.